stopbefore parameter error

[ruiguo-bio]

I use stopBefore=correction, but canu says ERROR: Invalid stopBefore specified (correction); must be one of: ERROR: 'gatekeeper' ERROR: 'meryl' ERROR: 'trimReads' ERROR: 'splitReads' ERROR: 'red' ERROR: 'oea' ERROR: 'unitig' ERROR: 'consensusConfigure' ERROR: 'cns'

[brianwalenz]

Those are mostly for debugging, and are hit-or-miss as to what is implemented. What are you trying to do?

[ruiguo-bio]

I want to just generate read overlap using mhap or ovl, so the correction read is not important. Sometimes canu stuck in the correction phase, so I want to stop before correction.

[brianwalenz]

Try stopAfter=overlapStore. This will generate overlaps and load them into the store. Also use saveOverlaps=true to save the raw output of the overlapper if you want it.

There is currently no way to stop after overlaps are computed but before they're loaded into the store - you can just kill canu when it starts building the store if you don't want it.

[ruiguo-bio]

That works, thank you!